Published May 12, 2023
| Version v1
Dataset
Open
Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations
Authors/Creators
Description
- 1-initial_topologies_coordinates.tar.gz
- primary input coordinates and parameter-topology files of all initial systems (LinBwt, LinB32, and Linb86 variants of haloalkane dehalogenase) in OPC and TIP3P water models
- prepared with the tleap module of AMBER18 package
- parm7 and crd formatted
- 2-cap_domain_gate_distances.tar.gz
- datasets with minimum distance calculation between Asp146 and Leu176
- calculated by CPPTRAJ module of AMBER 18 for each performed simulation
- plain text formatted
- 3-protein_trajectories-linbwt.tar.gz
- three replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of LinBwt in OPC and Tip3P water models with corresponding parameter-topology files
- produced by pmemd.cuda module of AMBER 18
- netcdf and parm7 formatted
- 3-protein_trajectories-linb32-closed.tar.gz
- two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of closed state LinB32 in OPC and Tip3P water models with corresponding parameter-topology files
- produced by pmemd.cuda module of AMBER 18
- netcdf and parm7 formatted
- 3-protein_trajectories-linb32-open.tar.gz
- two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of open state LinB32 in OPC and Tip3P water models with corresponding parameter-topology files
- produced by pmemd.cuda module of AMBER 18
- netcdf and parm7 formatted
- 3-protein_trajectories-linb86-closed.tar.gz
- two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of closed state LinB86 in OPC and Tip3P water models with corresponding parameter-topology files
- produced by pmemd.cuda module of AMBER 18
- netcdf and parm7 formatted
- 3-protein_trajectories-linb86-open.tar.gz
- two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of open state LinB86 in OPC and Tip3P water models with corresponding parameter-topology files
- produced by pmemd.cuda module of AMBER 18
- netcdf and parm7 formatted
- 4-basic_analyses.tar.gz
- datasets on RMSF, RMSD, RoG, and RDF from the CPPTRAJ module of AMBER 18
- representative structures from TTCLust
- for selected replicas 3x LinBwt, 2x LinB32-closed, 2x LinB32-open, 2x LinB86-closed and 2x LinB86-open
- plain text and PDB formatted
- 5-tunnel_networks-linbwt.tar.gz
- results of tunnel analyses for three replicas of LinBwt in OPC and TIP3P
- generated by CAVER 3.0
- comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt)
- plain text formatted
- 5-tunnel_networks-linb32-closed.tar.gz
- results of tunnel analyses for two replicas of closed state LinB32 in OPC and TIP3P
- generated by CAVER 3.0
- comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt)
- plain text formatted
- 5-tunnel_networks-linb32-open.tar.gz
- results of tunnel analyses for two replicas of open state LinB32 in OPC and TIP3P
- generated by CAVER 3.0
- comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt)
- plain text formatted
- 5-tunnel_networks-linb86-closed.tar.gz
- results of tunnel analyses for two replicas of closed state LinB86 in OPC and TIP3P
- generated by CAVER 3.0
- comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt)
- plain text formatted
- 5-tunnel_networks-linb86-open.tar.gz
- results of tunnel analyses for two replicas of open state LinB86 in OPC and TIP3P
- generated by CAVER 3.0
- comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt)
- plain text formatted
- 6-representative_tunnels.tar.gz data
- for visualization of representative tunnels named as p1b, p1a, p2a, p2b, p2c, p3
- generated by TransportTools library 0.9.5
- for selected replicas 3x LinBwt, 2x LinB32-closed, 2x LinB32-open, 2x LinB86-closed and 2x LinB86-open
- PDB formatted data with Pymol-based visualization scripts in Python 3.8 or higher
Notes
This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548) and ERDF
postdoc grant (no.1.1.1.2/VIAA/4/20/757). The computations were performed at the Poznan Supercomputing and Networking Center.
Files
readme.txt
Files
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Additional details
Related works
- Is described by
- Preprint: 10.1101/2023.04.19.537534 (DOI)